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New functions: - splot_PA: single-comparison patchwork plot (NES + FDR + MSigDB collections) - multiplot_PA: multi-comparison faceted barplot with comparison_order param - heatmap_PA: leading edge heatmaps from R objects - heatmap_path_PA: leading edge heatmaps from file paths - getgenesPA: extract leading edge or all genes per gene set - addgenesPA: append all_genes and/or le_genes columns to pa_data Updated: - merge_PA: add fdr_replace param, return data frame, validate Comparison column, fix globalVariables, improve documentation - plot_PA.R split into splot_PA + multiplot_PA - Simplified FDR: always computed internally as tmp_log10FDR
Updated functions (plot_PA.R): - getgenesPA: 'top'variable in genes parmater (user-defined rank-based fraction) - addgenesPA: append also top_genes columns to pa_data - heatmap_PA: add top_genes support in plot_genes parameter New example dataset (data-raw/gsea_results.R): - gsea_results: simulated merge_PA() output, 40 gene sets x 3 comparisons (TumorVsNormal, MetastasisVsNormal, MetastasisVsTumor), 3 collections (HALLMARK, KEGG, GO), ~60% FDR < 0.05 per comparison Documentation: - getgenesPA: add GSEA User Guide definition of tags, le vs top distinction, list_gmts reference in geneset_list param - addgenesPA: add top description - heatmap_PA: update examples using gsea_results and camera_results
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